[2023-07-01 06:01:20,897] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:01:20,908] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:01:20,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgb70c3d44-2698-4f54-9c3d-e8080318a181/dqc_reference
[2023-07-01 06:01:22,342] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:01:22,343] [INFO] Task started: Prodigal
[2023-07-01 06:01:22,343] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a2aeb59-5c05-4bf7-a6c7-1b2cf3af8475/GCA_019459185.1_ASM1945918v1_genomic.fna.gz | prodigal -d GCA_019459185.1_ASM1945918v1_genomic.fna/cds.fna -a GCA_019459185.1_ASM1945918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:01:30,587] [INFO] Task succeeded: Prodigal
[2023-07-01 06:01:30,587] [INFO] Task started: HMMsearch
[2023-07-01 06:01:30,587] [INFO] Running command: hmmsearch --tblout GCA_019459185.1_ASM1945918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb70c3d44-2698-4f54-9c3d-e8080318a181/dqc_reference/reference_markers.hmm GCA_019459185.1_ASM1945918v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:01:30,870] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:01:30,871] [INFO] Found 6/6 markers.
[2023-07-01 06:01:30,903] [INFO] Query marker FASTA was written to GCA_019459185.1_ASM1945918v1_genomic.fna/markers.fasta
[2023-07-01 06:01:30,904] [INFO] Task started: Blastn
[2023-07-01 06:01:30,904] [INFO] Running command: blastn -query GCA_019459185.1_ASM1945918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb70c3d44-2698-4f54-9c3d-e8080318a181/dqc_reference/reference_markers.fasta -out GCA_019459185.1_ASM1945918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:01:31,913] [INFO] Task succeeded: Blastn
[2023-07-01 06:01:31,917] [INFO] Selected 11 target genomes.
[2023-07-01 06:01:31,917] [INFO] Target genome list was writen to GCA_019459185.1_ASM1945918v1_genomic.fna/target_genomes.txt
[2023-07-01 06:01:31,918] [INFO] Task started: fastANI
[2023-07-01 06:01:31,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a2aeb59-5c05-4bf7-a6c7-1b2cf3af8475/GCA_019459185.1_ASM1945918v1_genomic.fna.gz --refList GCA_019459185.1_ASM1945918v1_genomic.fna/target_genomes.txt --output GCA_019459185.1_ASM1945918v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:01:40,589] [INFO] Task succeeded: fastANI
[2023-07-01 06:01:40,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb70c3d44-2698-4f54-9c3d-e8080318a181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:01:40,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb70c3d44-2698-4f54-9c3d-e8080318a181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:01:40,603] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:01:40,603] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 06:01:40,603] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	94.2937	716	892	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	87.6526	657	892	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	86.633	639	892	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	86.5274	678	892	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	86.141	666	892	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	85.6852	650	892	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	80.4002	479	892	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.3851	419	892	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	79.9761	406	892	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	79.9542	449	892	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	79.5305	480	892	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 06:01:40,606] [INFO] DFAST Taxonomy check result was written to GCA_019459185.1_ASM1945918v1_genomic.fna/tc_result.tsv
[2023-07-01 06:01:40,606] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:01:40,607] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:01:40,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb70c3d44-2698-4f54-9c3d-e8080318a181/dqc_reference/checkm_data
[2023-07-01 06:01:40,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:01:40,651] [INFO] Task started: CheckM
[2023-07-01 06:01:40,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019459185.1_ASM1945918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019459185.1_ASM1945918v1_genomic.fna/checkm_input GCA_019459185.1_ASM1945918v1_genomic.fna/checkm_result
[2023-07-01 06:02:11,240] [INFO] Task succeeded: CheckM
[2023-07-01 06:02:11,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 06:02:11,263] [INFO] ===== Completeness check finished =====
[2023-07-01 06:02:11,264] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:02:11,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019459185.1_ASM1945918v1_genomic.fna/markers.fasta)
[2023-07-01 06:02:11,265] [INFO] Task started: Blastn
[2023-07-01 06:02:11,265] [INFO] Running command: blastn -query GCA_019459185.1_ASM1945918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb70c3d44-2698-4f54-9c3d-e8080318a181/dqc_reference/reference_markers_gtdb.fasta -out GCA_019459185.1_ASM1945918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:02:13,080] [INFO] Task succeeded: Blastn
[2023-07-01 06:02:13,085] [INFO] Selected 11 target genomes.
[2023-07-01 06:02:13,085] [INFO] Target genome list was writen to GCA_019459185.1_ASM1945918v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:02:13,092] [INFO] Task started: fastANI
[2023-07-01 06:02:13,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a2aeb59-5c05-4bf7-a6c7-1b2cf3af8475/GCA_019459185.1_ASM1945918v1_genomic.fna.gz --refList GCA_019459185.1_ASM1945918v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019459185.1_ASM1945918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:02:21,055] [INFO] Task succeeded: fastANI
[2023-07-01 06:02:21,065] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 06:02:21,065] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000747075.1	s__Arenimonas malthae	94.2972	715	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	93.8154	558	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCA_001724815.1	s__Arenimonas sp001724815	87.7102	673	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	87.686	655	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747155.1	s__Arenimonas metalli	86.6634	637	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643775.1	s__Arenimonas soli	86.5451	677	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	86.1325	666	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743535.1	s__Arenimonas donghaensis	85.6683	651	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993735.1	s__Arenimonas daejeonensis	85.6641	645	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241895.1	s__Arenimonas sp003241895	85.0461	622	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	79.9124	431	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-07-01 06:02:21,067] [INFO] GTDB search result was written to GCA_019459185.1_ASM1945918v1_genomic.fna/result_gtdb.tsv
[2023-07-01 06:02:21,068] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:02:21,089] [INFO] DFAST_QC result json was written to GCA_019459185.1_ASM1945918v1_genomic.fna/dqc_result.json
[2023-07-01 06:02:21,089] [INFO] DFAST_QC completed!
[2023-07-01 06:02:21,089] [INFO] Total running time: 0h1m0s